Next-generation genome sequencing of families afflicted by mental disorders is identifying thousands of mutations with variable effect on disease risk. Two main problems that genetic community is facing before it could move forward with translating their findings into disease mechanisms are: (1) how to distinguish the pathogenic disease-causative mutations from the neutral ones? (2) what biological function(s) does each pathogenic mutation disrupt to cause a disease? These are fundamental questions that need urgent attention. The large number of identified mutations and functional heterogeneity of the affected genes do not permit developing a generalized experimental high-throughput method for addressing these problems. Although modern technologies (such as CRISPR) provide hope for the future in this direction, there is still a long way before we are able to apply it to thousandsof mutations. Thus, predictive computational approaches that aid in genes and mutations prioritization and functional characterization are needed. Here, we propose to develop such methods and apply them to coding and non-coding variants identified in families with Autism Spectrum Disorders (ASD). Our ASD-focused model of genetic variant impact will integrate heterogeneous genetic data with brain-specific functional data sources, such as gene expression and brain splice isoform interaction networks that are uniquely tailored towards brain processes. The unique feature of our approach is that it starts with prediction of biological function of a protein encoded by a gene carrying mutation(s), proceeds with gene and variant prioritization and functional impact assignment, and ends with a risk model for early ASD diagnosis. We will accomplish these goals through the following specific aims: (1) Predicting Biological Function of Genes and Autism-Specific Candidate Gene Prioritization; (2) Predicting Functional Impact of Coding and Non-coding Variants Conferring High Risk for ASD; (3) Experimental Validation of Predictions by Characterizing the Effect of Mutations on Protein Interactions, Transcription and Translation; (4) Developing Algorithms for Estimating ASD Risk from the Exome or Genome Sequence. This is as a novel approach in ASD research that combines expertise from diverse areas of molecular psychiatry, molecular biology and computational biology. The broad range of expertise by the investigators and their collaborators ensures a principled and comprehensive approach to the problem.